While the existence of skin-associated bacteria and fungi has been long-documented with culture-based studies, genomic sequencing studies enable identification of fastidious organisms and the simultaneous study of individual species and microbial communities. My laboratory has performed foundational studies of both the skin microbial (bacterial, fungal, viral) communities of healthy volunteer. We have developed marker based studies utilizing 16S rRNA and ITS to study bacteria and fungi, respectively. We have continued these analysis with shotgun metagenomic studies to simultaneously interrogate the bacterial, fungal, viral compositions of human skin. We track both species and strains and explore the full gene encoding potential of the bacterial communities. We performed a longitudinal study to explore the stability of the skin microbial communities at the strain level. Our clinical studies have focused on children with moderate to severe atopic dermatitis (eczema), who often progress to develop other atopic disorders, such as allergic rhinitis (hay fever) and asthma. Our objective is to investigate whether microbial diversity might serve as a biomarker to predict a change in disease progression and to direct an individual patients treatment. Our human skin microbiome research is carried out under clinicaltrials.gov NCT00605878; PI: Segre. We analyzed the composition of bacterial communities during AD disease states to identify characteristics associated with AD flares and improvement post-treatment. Disease severity was assessed quantitatively with SCORAD (SCORing AD), a well-validated clinical tool. We explored microbial temporal dynamics with metagenomic sequencing to investigate the role of staphylococci in AD. Species-level investigation of AD flares demonstrated a microbial dichotomy in which S. aureus was predominant on more severely affected patients while S. epidermidis was more predominant on less severely affected patients. Metagenomic analyses at the strain-level determined that S. aureus-predominant patients were monocolonized with distinct S. aureus strains, while all patients had heterogeneous S. epidermidis strain communities. To assess the immunologic effects of these species, we topically applied patient-derived strains to mice. AD strains of S. aureus were sufficient to elicit skin inflammation associated with specific immune cell infiltration, similar to features characteristic of AD patients. Integrating sequencing, culturing, and animal models, we explored a model whereby staphylococcal strains contribute to AD progression through activation of the host immune system. These findings demonstrate that, as compared to culture-based studies, higher resolution examination of microbiota associated with human disease provides novel insights into global shifts of bacteria relevant to disease progression and treatment. Mechanistically, we are assessing the skin microbiome's role in driving AD with animal models recapitulating the skin disorder. Future microbiome studies will integrate genetics of both host (human) and microbes, realizing that we are super-organisms with trillions of microbes living in and on our bodies. We explore the skin microbial diversity of patients with primary immune deficiency, a genetically defined subset of whom develop cutaneous warts and other viral infections. Shotgun metagenomic analysis of these patients has expanded the skin virome, identify hundreds of novel human papillomaviruses. We are developing studies to understand the skin colonization of an emerging human pathogen, Candida auris.